Explore ATLAS Installation in local machine

[vasanthi014]

https://github.com/OHDSI/Atlas

[shossain-mizzou]

• [x] OHDSI Atlas
• [x] OHDSI WebAPI https://github.com/OHDSI/WebAPI
• [x] OHDSI CommonDataModel
• [x] OHDSI OMPO CDM population (Synthetic Data) https://github.com/OHDSI/ETL-Synthea
• [x] OHDSI ACHILLIES
• [x] OHDSI DataSource Configuration https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration
• [x] Add Vocabulary https://github.com/OHDSI/Vocabulary-v5.0

[vasanthi014]

OMOP_CDM database has MU PCORnet data converted to OMOP CDM format

[shossain-mizzou]

https://github.com/synthetichealth/synthea/wiki/Developer-Setup-and-Running

[shossain-mizzou]

Data can be generated: https://github.com/synthetichealth/synthea Already generated: https://github.com/synthetichealth/synthea-sample-data/blob/master/downloads/synthea_sample_data_csv_nov2021.zip

[shossain-mizzou]

Steps:

1. Prepare Databases

WebAPI Database:

• create db: ohdsi_webapi
• create schema: webapi

OMOP CDM Database:

• create db: omop_cdm
• create schema: cdm, results, temp, native

2. OHDSI Atlas

• Build and run dockerfile in Atlas repository. [Port Mapping: 80:8080] [ENV: WEBAPI_URL=http://<ip/dns>:8080/WebAPI/]

3. OHDSI WebAPI:

• Modify profile: webapi-docker in pom.xml and add webapi database credential
• Modfile security configuration in pom.xml: https://github.com/OHDSI/WebAPI/wiki/Security-Configuration
• Build and run dockerfile in Webapi repository. [Port Mapping: 8080:8080]

4. Post-deployment database configurations:

OMOP CDM Database:

• create cdm tables using ETL_OMOP ddl.R script from this repository.
• populate vocuabulary tables using above scripts
• populate synthetic using above script / real data
• Run Achilles: https://github.com/OHDSI/Achilles/blob/main/vignettes/RunningAchilles.Rmd

WebAPI Database

• Running WebAPI will create ddl for webapi schema in ohdsi_webapi
• Once tables are created, need to add data sources: https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration
• curl -X GET "http://:8080/WebAPI/ddl/results?dialect=postgresql&schema=results&vocabSchema=cdm&tempSchema=temp&initConceptHierarchy=true" -o OMOPCDM_GENERATE.sql and execute queries in OMOP_CDM
• Refresh datasource: curl -X GET "http://:8080/WebAPI/source/refresh"
• Validation: curl -X GET "http://:8080/WebAPI/source/sources"